[Freesurfer] mri_label2label dependencies

External Email - Use Caution Dear freesurfers, I am using mri_label2label with -regmethod volume . The only other switches I am using are minimal as you can see below. The thing is that none of the freesurfer stuff is in the srcsubject's directory. Why is there no error

Re: [Freesurfer] mris_smooth error: can't allocate region

External Email - Use Caution Hi Bruce, This is the FS version: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c I reinstalled the MATLAB. Do you think this will result in the issue? Thanks, PH On Wed, Aug 22, 2018 at 4:12 PM Bruce Fischl wrote: > what version of FS are you

Re: [Freesurfer] selxavg3-sess contrasts error

External Email - Use Caution Thank you! It was a format problem. Best Francesca Il giorno mer 22 ago 2018 alle ore 17:51 Douglas N. Greve < dgr...@mgh.harvard.edu> ha scritto: > There is something wrong with the paradigm file (-par when running > mkanalysis-sess). Check the

Re: [Freesurfer] mris_smooth error: can't allocate region

what version of FS are you using? I think this is a bug that we had years ago for only a few weeks. One workaround would be to load each .mgz volume into matlab and write them back out (which will strip all the tags from them). I'm not sure why you are having the problem though Bruce On Wed,

Re: [Freesurfer] Flipped left to right hemisphere subjects

You can use mri_convert with the --left-right-reverse-pix option On 08/22/2018 02:55 PM, Lutz,Olivia (BIDMC - Psychiatry) wrote: > Hi Doug, > If you are talking about the brainmask, then yes that volume is left-right  > reversed as well as the nu.mgz. > > Thanks! > Olivia > > Greve, Douglas

Re: [Freesurfer] Manually editing location of surface

External Email - Use Caution The subject in particular is in their 90's. I have been seeing a similar occurrence in many of my other subjects as well. I will be attaching a link through google drive to share the subject I recently sent. (

Re: [Freesurfer] Flipped left to right hemisphere subjects

Hi Doug, If you are talking about the brainmask, then yes that volume is left-right reversed as well as the nu.mgz. Thanks! Olivia Greve, Douglas N.,Ph.D. Mon, 20 Aug 2018 14:44:00

Re: [Freesurfer] Histogram analysis capability via mri_segstats or other command-lines in Freesurfer?

If you load in a surface, then use the annotation (read_annotation.m, there are lots of docs in the mfile) On 08/22/2018 12:18 PM, Yash Patel wrote: > > External Email - Use Caution > > Hi Dr.Greve, > > I ran: > seg = MRIread('aparc+aseg.mgz'); > > input = MRIread('surface_pf05.mgh'); >

Re: [Freesurfer] mris_smooth error: can't allocate region

External Email - Use Caution Hi Douglas, Yes, I did try similar way to see if it worked. I deleted the whole folder and re-ran it. It stoped at the same place. Is there any other suggestion I could try? Thanks, PH On Wed, Aug 22, 2018 at 1:23 PM Douglas N. Greve wrote: > It

Re: [Freesurfer] mris_smooth error: can't allocate region

It looks like a corrupted file. Try renaming/deleting lh.orig.nofix, regenerating it, then seeing if mris_smooth works. On 08/22/2018 10:44 AM, Paysing Wu wrote: > > External Email - Use Caution > > Hi FreeSurfer Developers, > > I was running recon-all and it stoped at smooth1. The

Re: [Freesurfer] Histogram analysis capability via mri_segstats or other command-lines in Freesurfer?

no, that won't work as the discretization to a volume will mess everything up. If you really want the intensities at the midpoint, I would use mris_expand to generate a halfway surface, then use that surface for vol2surf. Then you can load the resulting .mgz 'volume' into matlab and computed

Re: [Freesurfer] Histogram analysis capability via mri_segstats or other command-lines in Freesurfer?

External Email - Use Caution Hi, I need to input a surface file, an output from mri_vol2surf --projfrac 0,5 Would doing mri_vol2surf, and then mri_surf2vol - turning it back into a volume file be a reasonable approach? Thanks, Yash On Wed, Aug 22, 2018 at 12:31 PM, Bruce Fischl

Re: [Freesurfer] Histogram analysis capability via mri_segstats or other command-lines in Freesurfer?

Hi Yash try something like: seg = MRIread('aparc+aseg.mgz'); norm = MRIread('norm.mgz'); ind = find(seg.vol == 1002); segmode = mode(norm.vol(ind)) cheers Bruce On Wed, 22 Aug 2018, Yash Patel wrote: External Email - Use Caution Hi Dr.Greve, I ran:  seg =

Re: [Freesurfer] Histogram analysis capability via mri_segstats or other command-lines in Freesurfer?

External Email - Use Caution Hi Dr.Greve, I ran: seg = MRIread('aparc+aseg.mgz'); input = MRIread('surface_pf05.mgh'); ind = find('aparc+aseg.mgz' == 1002); #where 1002 is a roi number segmode = mode(input(ind)); This is where i run into an error: Index exceeds array bounds.

Re: [Freesurfer] Calculating Gray Matter Density

That paper does not use FreeSurfer. We don't  have a way to compute "density". Usually this is used in the context of VBM, but I don't see that mentioned in the paper either. On 08/21/2018 05:01 PM, Andrew Jahn wrote: > > External Email - Use Caution > > Hello, > > Does FreeSurfer have

Re: [Freesurfer] selxavg3-sess contrasts error

There is something wrong with the paradigm file (-par when running mkanalysis-sess). Check the paradigm file for this subject and run. On 08/22/2018 10:16 AM, Francesca Strappini wrote: > > External Email - Use Caution > > Hi, > > I'm trying to analyze a block-design experiment. I run

Re: [Freesurfer] bbregister error

Can you send the terminal output and/or the log file? On 08/22/2018 09:49 AM, Nada Naguib wrote: > > External Email - Use Caution > > Hello, thank you for your response, yes My terminal is in the tcsh > shell so I’m not sure why it’s not working > > Nada > > > On Aug 22, 2018, at 3:22

Re: [Freesurfer] Manually editing location of surface

wow, looks like a pretty serious failure (which we rarely see). If you tar, gzip and ftp the entire subject dir for this subject we will take a look cheers Bruce On Tue, 21 Aug 2018, Elena Nicole Dominguez wrote: External Email - Use Caution Thank you for getting back to

Re: [Freesurfer] Histogram analysis capability via mri_segstats or other command-lines in Freesurfer?

Hi Yash we already create the volumetric representations for you (e.g. the aparc+aseg.mgz). You should be able to use it to generate histograms of each parcel in 5-10 lines of matlab code cheers Bruce On Wed, 22 Aug 2018, Yash Patel wrote: External Email - Use Caution

Re: [Freesurfer] Histogram analysis capability via mri_segstats or other command-lines in Freesurfer?

External Email - Use Caution Hi FS experts, I am attempting to extract signal intensity from the middle of the cortex, using mri_vol2surf. With said surface, I would like to extract the mode (and other histogram measures) from each of the 34 parcellations of the DK atlas. I

[Freesurfer] ERROR: make_roi_paths did not complete successfully!

External Email - Use Caution Hello FreeSurfer Developers, I am attempting to compute the local gfrification index(LGI), but is comes errors as below: my command line is: recon-all -lgi -s AD02 INFO: current FREESURFER_HOME does not match that of previous

Re: [Freesurfer] bbregister error

External Email - Use Caution Hello, thank you for your response, yes My terminal is in the tcsh shell so I’m not sure why it’s not working Nada > On Aug 22, 2018, at 3:22 PM, Adam Martersteck wrote: > > External Email - Use Caution > > Are you sure you're

Re: [Freesurfer] bbregister error

External Email - Use Caution Are you sure you're terminal is setup in tcsh or csh? If you're using bash instead, you want "export SUBJECTS_DIR=/project/bil/Nada" Take a look at: https://surfer.nmr.mgh.harvard.edu/fswiki/SetupConfiguration_Mac or

[Freesurfer] selxavg3-sess contrasts error

External Email - Use Caution Hi, I'm trying to analyze a block-design experiment. I run selxavg3-sess: selxavg3-sess -s MS -analysis MS_VisLocDrawings.sm03.rh And I got this error message while computing the contrasts. Any idea what does it mean? outtop =

[Freesurfer] bbregister error

External Email - Use Caution Hello, I have been using bbregister in this format bbregister —mov dkti4d.nii —s NewT2out —init-fsl —bold —lea register.lta NewT2out is the output of the free surfer processing on the T1 image and dkti4d.nii is the template file I want to use for